SMTL ID : 6cri.1

Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-3-6-3-3-3-mer

Ligands

6 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 18 residues within 4Å: Chain C: D.10, A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, D.51, G.53, K.111, D.113, A.144, T.145 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:A.11, C:A.12, C:G.13, C:K.14, C:T.15, C:T.15, C:T.16, C:T.16, C:T.32, C:T.32, C:T.32, C:A.144, C:T.145 Salt bridges: C:K.14, C:K.14, C:D.113 GTP.3: 19 residues within 4Å: Chain E: A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, G.53, L.55, N.110, K.111, D.113, C.143, A.144, T.145 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:A.11, E:A.12, E:G.13, E:K.14, E:T.15, E:T.15, E:T.15, E:T.16, E:T.16, E:T.32, E:T.32, E:G.54, E:N.110, E:K.111, E:A.144, E:T.145 Salt bridges: E:D.113 GTP.5: 18 residues within 4Å: Chain K: D.10, A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, D.51, G.53, K.111, D.113, A.144, T.145 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain K Hydrogen bonds: K:A.11, K:A.12, K:G.13, K:K.14, K:T.15, K:T.15, K:T.16, K:T.32, K:T.32, K:T.32, K:A.144, K:T.145 Salt bridges: K:K.14, K:K.14, K:D.113 GTP.7: 19 residues within 4Å: Chain M: A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, G.53, L.55, N.110, K.111, D.113, C.143, A.144, T.145 Ligands: MG.8 17 PLIP interactions: 17 interactions with chain M Hydrogen bonds: M:A.11, M:A.12, M:G.13, M:K.14, M:T.15, M:T.15, M:T.16, M:T.16, M:T.29, M:T.32, M:T.32, M:G.54, M:N.110, M:K.111, M:A.144, M:T.145 Salt bridges: M:D.113 GTP.9: 18 residues within 4Å: Chain S: D.10, A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, D.51, G.53, K.111, D.113, A.144, T.145 Ligands: MG.10 16 PLIP interactions: 16 interactions with chain S Hydrogen bonds: S:A.11, S:A.12, S:G.13, S:K.14, S:T.15, S:T.15, S:T.15, S:T.16, S:T.32, S:T.32, S:T.32, S:A.144, S:T.145 Salt bridges: S:K.14, S:K.14, S:D.113 GTP.11: 19 residues within 4Å: Chain U: A.11, A.12, G.13, K.14, T.15, T.16, T.29, I.30, P.31, T.32, G.53, L.55, N.110, K.111, D.113, C.143, A.144, T.145 Ligands: MG.12 16 PLIP interactions: 16 interactions with chain U Hydrogen bonds: U:A.11, U:A.12, U:G.13, U:K.14, U:T.15, U:T.15, U:T.16, U:T.16, U:T.32, U:T.32, U:G.54, U:N.110, U:K.111, U:A.144, U:T.145 Salt bridges: U:D.113

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain C: T.15, T.32 Ligands: GTP.1 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.15, C:T.32 MG.4: 3 residues within 4Å: Chain E: T.15, T.32 Ligands: GTP.3 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.15, E:T.32 MG.6: 3 residues within 4Å: Chain K: T.15, T.32 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:T.15, K:T.32 MG.8: 3 residues within 4Å: Chain M: T.15, T.32 Ligands: GTP.7 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:T.15, M:T.32 MG.10: 3 residues within 4Å: Chain S: T.15, T.32 Ligands: GTP.9 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:T.15, S:T.32 MG.12: 3 residues within 4Å: Chain U: T.15, T.32 Ligands: GTP.11 2 PLIP interactions: 2 interactions with chain U Metal complexes: U:T.15, U:T.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morris, K.L. et al., HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Cell (2018)

Release Date

2018-08-01

Peptides

Bone marrow stromal antigen 2, Protein Nef chimera: AHIPQX
AP-1 complex subunit beta-1: BJR
ADP-ribosylation factor 1: CEKMSU
AP-1 complex subunit gamma-1: DLT
AP-1 complex subunit mu-1: FNV
AP-1 complex subunit sigma-3: GOW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

H
N

I
c

P
Y

Q
d

X
Z

B
B

J
I

R
J

C
C

E
H

K
K

M
U

S
L

U
V

D
G

L
Q

T
R

F
M

N
W

V
X

G
S

O
a

W
b

Bone marrow stromal antigen 2, Protein Nef chimera

AP-1 complex subunit beta-1

ADP-ribosylation factor 1

AP-1 complex subunit gamma-1

AP-1 complex subunit mu-1

AP-1 complex subunit sigma-3

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